As of 2008 the CDC estimated that there were approximately 1.1 million persons in the U.S. infected with HIV- 1 and about 56,000 new cases are diagnosed each year. During the mid-to-late 1990s, advances in treatment slowed the progression of HIV to AIDS and related deaths. Unfortunately, the treatment often leads to the emergence of drug resistant mutants of HIV-1. The knowledge of the HIV-1 variants present in a patient is extremely important to effectively plan disease management. It is estimated that about 10% of HIV-1 infections in the US is caused by drug resistant HIV-1 variants and current guidelines recommend HIV-1 resistance genotyping before therapy and to monitor therapy effectiveness. However, current tests that rely on conventional DNA sequencing methods do not detect low-levels (<20%) of drug-resistant strains and therefore may not provide the necessary diagnostic information for effective treatments. The goal of this proposal is to develop a highly sensitive comprehensive and cost-effective system for HIV-1 resistance genotyping based on IBS' high-speed massively parallel DNA sequencing system (RESIQ). IBS' sequencing-by-synthesis system is based on the use of cleavable fluorescent nucleotides with reversible terminator technology. These features enable efficient removal of fluorescent signals and sequencing of repeats. During Phase II, a prototype sequencing instrument prototype will be constructed and extensive validation of the prototype using validated clinical samples will be performed. Dr. Daniel Kuritzkes, an expert in the HIV-1 treatment and resistance will serve as a consultant for this project. Successful accomplishment of the Phase II project will result in the development of highly effective and comprehensive RESIQ system for rapid, sensitive cost-effective HIV-1 drug resistance genotyping. 0